MolNFT v1 · #93352 · protein

Crystal structure of a lipocalin family protein (BACOVA_00364) from bacteroides ovatus atcc 8483 at 1.95 a resolution

4GZV · Hypothetical protein: “Crystal structure of a lipocalin family protein (BACOVA_00364) from bacteroides ovatus atcc 8483 at 1.95 a…”. X-ray diffraction, 2 ligands (UNL, NA), 15 pockets (best druggability 0.80). MolNFT v1 #93352 on…

PDB: 4GZV
Type: protein
Length: 1,084 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein
UniProt: A7LRD6
Ligands: UNL, NA
Pockets: 15 · best druggability 0.80

Structure

x-ray diffraction · 5 distinct chains · 3% helix, 59% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein	protein	139	4% helix, 58% strand	A7LRD6
B, D	Hypothetical protein	protein	133	2% helix, 61% strand	A7LRD6
C, F, G	Hypothetical protein	protein	136	2% helix, 60% strand	A7LRD6
E	Hypothetical protein	protein	141	2% helix, 57% strand	A7LRD6
H	Hypothetical protein	protein	130	2% helix, 58% strand	A7LRD6

Ligands and binding sites

UNL · Unknown ligand · ligand · 5 copies · chains A, C, B, D, E, G, F, H
NA · Sodium ion · metal · chains F
GOL · Glycerol · additive · 4 copies · chains B, C, E, H
ACT · Acetate ion · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1027	0.80	0.82	87	empty
2	1185	0.80	0.81	103	empty
3	365	0.64	0.79	39	empty
4	305	0.60	0.78	35	empty
5	284	0.58	0.78	36	empty

Interfaces

14 interfaces between chains.

E–G · 1988 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 1979 Å² buried · 22 hydrogen bonds · protein-protein
B–D · 1950 Å² buried · 19 hydrogen bonds · protein-protein
F–H · 1938 Å² buried · 20 hydrogen bonds · protein-protein
F–G · 607 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

4GZV · Crystal structure of a lipocalin family protein (BACOVA_00364) from Bacteroides ovatus… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A7LRD6
Elsewhere: RCSB PDB 4GZV · PDBe 4GZV · UniProt A7LRD6

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